title: Bb_2

city: shanghai

first: zhenghui

last: hong

state: --- Select a state ---

address: dongchuan road NO.800

department: life of science

country: China

institute: shanghai jiaotong university

description: genes.fpkm

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: http://plants.ensembl.org/Arabidopsis_thaliana/Info/Index
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: seedling

extract_protocol:
Seedlings were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: seedlings day 12

tag: genotype


title: Leaf_control_WT_rep1

status: Public on Nov 01 2019

type: RNA

city: Guelph

first: JOSE

middle: A

last: CASARETTO

state: ON

address: 50 Stone Road E

department: MCB

country: Canada

institute: University of Guelph

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >12.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to 4x44K Rice Gene Expression Microarray for 16 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed with Wash Buffer 1 (Agilent) for 1 minute at room temperature followed by another wash with Wash buffer 2 (Agilent) for 1 minute, then dried by centrifugation. (Service provided by ImaGenes GmbH, Berlin, Germany).

scan_protocol: Microarray slides were scanned on a Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan resolution 10 um, Dye channel is set to Green and Green PMT is set to 100%). (Service provided by ImaGenes GmbH, Berlin, Germany).

data_processing: Scanned images were analyzed with the Feature Extraction Software 9.0 (Agilent) using default parameters to obtain background subtracted plus the spatially detrended processed signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. (Service provided by ImaGenes GmbH, Berlin, Germany).

molecule: total RNA

organism: Oryza sativa

source_name: leaf, wild-type

label_protocol: Cy3-labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer. (Service provided by ImaGenes GmbH, Berlin, Germany).

growth_protocol: Plants were grown in 1-L pots with an inert mix of clay:vermiculite (1:1) as substrate and fertilized with nutrient solution. Plants were grown in chambers in a 16 h daylight photoperiod and at a 30°C/20°C day/night cycle.

extract_protocol: Extraction of total RNA from leaves was carried out with the TRIZOL® method (Invitrogen) following the manufacturer's recommendations and then treated with RNase-free DNase I (Ambion). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: No treatment prior RNA extraction

tag: tissue

value: leaf


title: Bb_3

type: SRA

description: genes.fpkm

library_source: transcriptomic

organism: Arabidopsis thaliana

tag: strain

value: Columbia

tag: age


title: Ba_3

description: genes.fpkm


title: AG1296-10uM-treated rep2

city: Westmead

first: Ashley

last: Waardenberg

state: NSW

address: 214 Hawkesbury Road

country: Australia

institute: Children's Medical Research Institute

description:
AG1296_10M_Rep2
Gene expression data from cCFU-Fs treated with 10uM AG1296

hyb_protocol: 3.52 ug of fragmented labelled ssDNA was hybridised to Mouse Gene 1.0 ST Gene Arrays  for 16 hours at 45°C in the Affymetrix GeneChip Oven. Arrays were washed on the Affymetrix Fluidics 450 instrument as per manufacturer’s protocol using the Affymetrix GeneChip Hybridization Wash & Stain kit for cartridge arrays.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip 3000 7G Scanner instrument as per manufacturer’s protocol

data_processing: Affymetrix GeneChip Command Console (AGCC) software was used to generate the CEL files from the DAT image files. All analyses were performed in R, using the affy, affyPLM and limma libraries. Data were Robust Multichip Average (RMA) normalised.

label: biotin

organism: Mus musculus

source_name: cCFU-F_AG1296 treated with 10uM

label_protocol: 100ng of total RNA was labelled using the Affymetrix WT kit (Ambion).

growth_protocol: Primary cells were isolated from the Bl6 mice and cultured at 37oC and 5% CO2.

extract_protocol: Total RNA was extracted using RNAeasy micro RNA isolation kit (Qiagen) and the quality of RNA was assessed using the Nanodrop (Thermofisher Scientific; 230/260>1.8, 260/280>1.8) and Bioanalyzer (Agilent, RIN>8.0). The RNA was then sent to the Ramaciotti Center for Genomics (University of New South Wales, Sydney) for further processing.

treatment_protocol: Cultured cells were treated with 1um/10uM of AG1296, PDGF-AB (50ng/ml) or untreated.

value: 12 weeks

tag: Sex

value: male

tag: cell type

value: cardiac colony forming units - fibroblast (cCFU-F)

tag: isolated cardiac cells

value: SCA1+PDGFRα+CD31- (S+P+)

tag: treated with


title: Bb_1

description: genes.fpkm


title: Ba_2

description: genes.fpkm


title: B_1

description: genes.fpkm


title: D1 undifferentiated

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

country: Germany

institute: Helmholtz Zentrum München

data_processing:
STAR aligner was used for split-read alignment against the mouse genome assembly mm9 and UCSC known Gene annotation. To quantify the number of reads mapping to annotated genes, we used HTseq-count.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *.htseqcounts.tsv: Tab-delimited text files contain raw read counts; they have two columns, where the first column specifies the gene name and the second the actual read count.

source_name: brown adipose tissue

growth_protocol: Murine brown pre-adipocytes were maintained in medium containing glucose, pyruvate, FBS and Pen-Strep. Cells were split and replated every 2 days.

extract_protocol:
RNA was extracted with RNeasy kit (Qiagen) following manufacturer's instruction.
For library preparation, 1 µg of total RNA per sample was used. RNA molecules were poly(A) selected, fragmented, and reverse transcribed with the Elute, Prime, Fragment Mix (EPF, Illumina). End repair, A-tailing, adaptor ligation, and library enrichment were performed as described in the TruSeq Stranded mRNA Sample Preparation Guide (Illumina). RNA libraries were assessed for quality and quantity with the Agilent 2100 BioAnalyzer and the Quant-iT PicoGreen dsDNA Assay Kit (Life Technologies).
Strand-specific RNA libraries were sequenced as 100 bp paired-end runs on an Illumina HiSeq4000 platform.

treatment_protocol: IBMX, dexamethasone, indomethacin, T3 and insulin were added to induce differentiation. Cells were differentiated for 8 days, by subsequently changing medium (with T3 and insulin) every 2 days.

tag: strain/background

tag: cell line

value: immortalised brown adipose cells

tag: developmental stage

value: undifferentiated

tag: passage number


title: WT LL rep3

city: New Brunswick

first: Ananya

last: Agarwal

state: New Jersey

address: 71 Dudley Road

department: Microbial Biology

country: USA

institute: Rutgers, The State University of New Jersey

data_processing:
Sequenced reads were trimmed for adaptor sequence, and  for low-complexity or low-quality sequence, then mapped to Phaeodactylum tricornutum v3 whole genome using CLC Genomivs Workbench
Reads per exons for each sample were exported from CLC Genomic Workbench and served as the input to DESeq2 to infer differential gene expression between low and high light.
Genome_build: GCA_000150955.2
Supplementary_files_format_and_content: Raw read counts per gene.

organism: Phaeodactylum tricornutum

source_name: WT P.tricornutum cells

growth_protocol: maintained optically thin and axenically in sterile artificial seawater enriched with F/2 nutrients in the absence of Silica

extract_protocol:
RNA was harvested using TRIzol reagent followed by removal of DNA contamination using ThermoFisher Scientific TURBO DNA-free kit and cleaning with a Qiagen RNEasy MinElute Kit. Illumina TruSeq RNA Library Prep Kit v2  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols. The 250-bp single-indexed libraries were multiplexed and sequenced on an Illumina MiSeq platform

treatment_protocol: A set of three biologically independent cultures was acclimated to 20 and 940 quanta m-2s-1 and maintained under exponential growth conditions

value: wild type (WT)

tag: growth condition

value: Low Light (LL - 20 quanta m-2s-1)


title: Ba_1

description: genes.fpkm


title: WT HL rep3

value: High Light (HL - 940 quanta m-2s-1)


title: WT_2

description: genes.fpkm

value: wild type


title: WT LL rep1


title: Bone marrow stromal cells, S5545

city: Berlin

first: Karsten

last: Jürchott

address: Luisenstraße

department: Rahel Hirsch Center

institute: BIH at Charité

data_processing:
HiSeq Control Software 2.2.58,  Basecall: RTA 1.18.64.0
FastQ generation: bcl2fastq 1.8.4, FastQ trimming: Trimmomatic 0.36 (ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:3:20 MINLEN:36), alignment: tophat 2.1.0 with bowtie2 2.2.5 and samtools 0.1.19 (--no-novel-juncs)
Reads were summarized per gene using the featureCount algorithm implemented in the R package Rsubread (v1.16.1).
Raw counts of protein-coding genes were normalized either using varianceStabilizingTransformation or normTransform function of the DESeq2 package (v1.6.3) (pseudocount=1, log2-transformation).
Genome_build: iGenome Homo_sapiens/Ensembl/GRCh38
Supplementary_files_format_and_content: Raw counts - tab-deliminated file with reads summerized per gene.
Supplementary_files_format_and_content: Variancestablized transformed data (vst) - tab-deliminated file with normalized and variance stabilizing transformed data of protein-coding genes
Supplementary_files_format_and_content: Normalized data (norm) - tab-deliminated file with normalized and log2-transformed data (pseudocount=1) of protein-coding genes

molecule: polyA RNA

organism: Homo sapiens

source_name: bone marrow stromal cells

growth_protocol: The cells were isolated from metaphyseal bone marrow (BM) biopsies from patients undergoing hip replacement at Charité University Hospital. Briefly, the BM mononuclear cell fraction (BM-MNC) in primary BM and the BMSC fraction post Ficoll-density gradient centrifugation (Histopaque 1077; Sigma-Aldrich) were quantified with an automated electrical impedance-based CASYR Cell Counter (Schaerfe System GmbH). The BMSCcontaining interphase was plated in a 300 cm2 tissue culture flask (ThermoFischer) and cultured under standard conditions (37◦C, 5% CO2) in an expansion medium (Dulbecco’s Modified Eagle Medium-Low Glucose [DMEM-LG; Sigma-Aldrich] containing 10% fetal calf serum [FCS; Biochrom AG], 100 U/mL penicillin, and 100μg/mL streptomycin [Biochrom AG], and 2mM L-alanyl-L-glutamine [GlutaMAX; Gibco]). The non-adherent fraction was removed by washing with PBS (Gibco), the medium was changed every 72 h, and the cells were allowed to reach about 80% confluence before passaging. The BMSCs were then expanded for several passages and were characterized with multiple functional and molecular assays, in line with the minimal criteria of the International Society for Cellular Therapy (ISCT) (69), at passage three (P3, early  passage) and six (P6, late passage).

extract_protocol:
Total RNA was extracted by using the Qiagen RNeasy Plus Mini Kit (Qiagen), according to the manufacturer’s instructions.
Poly-(A)-selection was performed utilizing the NEBNext Poly(A)mRNA Magnetic Isolation Module (NEB) according to the manufacturers requirements. mRNA libraries were prepared with the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB). All libraries were analyzed with the Agilent DNA 1000 Kit and quantified using the Qubit® dsDNA BR Assay Kit (ThermoFisher). After equimolar pooling all samples were sequenced on an Illumina HiSeq system with High Output chemistry v4 (50 cycles, single-read)

treatment_protocol: A subset of n = 7 donors was treated for 24 h with or without cytokines (TNF-alpha and IFN-gamma, both 10 ng/mL), which werematched to the corresponding unstimulated cells and processed in parallel.

tag: donor

tag: gender

value: M

tag: diabetes

value: h

tag: passage

tag: stimulation

value: REST

value: bone marrow-derived stromal cells (BMSC)


title: B_2

description: genes.fpkm

value: seedlings day 12

tag: genotype


title: B_3

description: genes.fpkm

tag: strain


title: Bone marrow stromal cells, S5681

tag: age


title: WT LL rep2


title: WT_1

description: genes.fpkm


title: iWAT sample.hfd_con1

city: St Louis

first: Charles

last: Harris

state: MO

address: 660 S. Euclid Ave

department: Department of Medicine

institute: Washington University School of Medicine in St. Louis

data_processing:
Basecalling and demultiplexing with Illumina RTA 3.4
Fastq files were aligned with STAR 2.5.1a
Gene counts dervied with Subread:featureCount 1.4.6p-5 and annotated with Ensembl Biomart
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: Gene counts, CPMs, RPKMs in tab-delimited text format

source_name: inguinal white adipose tissue

extract_protocol:
Tissues were flash frozen in liquid nitrogen.  RNA was extracted from tissues using TRIzol Reagent (Ambion) and Purelink™ RNA Mini Kit (Invitrogen™).  RNA integrity was validated by an Agilent bioanalyzer.
KAPA RiboErase

tag: diet/treatment

value: High Fat Diet

value: control (MRflox/flox )

tag: tissue

value: inguinal white adipose tissue


title: Bone marrow stromal cells, S5682

tag: cell type


title: WT_3

description: genes.fpkm

value: Columbia


title: iWAT sample.hfd_con2


title: OCI-LY1-C

city: columbus

first: Lalit

last: Sehgal

state: Ohio

department: Hematology

institute: The Ohio State University

description: Gene expression Parental

hyb_protocol: Hybridization was performed in Agilent’s SureHyb Hybridization Chambers. The labeled cRNAs were hybridized onto the Whole Human Genome Oligo Microarray (4 x 44K, Agilent Technologies). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

scan_protocol: After washing, slides were scanned with the Agilent DNA Microarray Scanner. Data was extracted using Agilent Feature Extraction software. Normalization was performed using Agilent GeneSpring GX 12.1 software. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images

data_processing: Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software (Agilent Technologies). After quantile normalization of the raw data, genes that at least 3 out of 24 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes were identified through Fold Change filtering and Volcano filtering. Pathway analysis and GO Analysis were applied to determine the roles of these differentially expressed genes played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable gene expression profiling among samples.Further data analysis was performed using Agilent GeneSpring GX 12.1 software. To identify differentially expressed genes, we performed a Fold Change filtering between two samples and a Volcano Plot filtering between two groups. The default threshold is Fold Change>=2.0, P-value<=0.05.

source_name: cell line parental rep 3

label_protocol: Agilent Quick Amp Labeling Kit was used for sample labeling. Briefly, total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies).

extract_protocol: Total RNA was isolated using Qiagen kits, following which Integrity and concentration of RNA was assessed after RNA extraction and prior to sample labeling.

treatment_protocol: The Cell lines were cultured at LD75 for over 8months and Ibrutinib resistant clones were selected and gene profiled.

value: GC-DLBCL

tag: drug (ibrutinib) sensitivity

value: Sensitive


title: WT HL rep1


title: WT HL rep2


title: iWAT sample.hfd_con3


title: D2 undifferentiated

tag: strain/background

value: immortalised brown adipose cells


title: Bone marrow stromal cells, S5546

value: F


title: Bone marrow stromal cells, S5547


title: iWAT sample.hfd_con4


title: Bone marrow stromal cells, S5548


title: OCI-LY-10-C

description: Gene expression Parental

tag: cell line

value: ABC-DLBCL


title: HBL-1-A

description: Gene expression Parental

source_name: cell line parental rep 1


title: C5 undifferentiated

tag: developmental stage

value: undifferentiated


title: Keratinocytes incubated with Epilife, biological replicate 2

city: London

first: Helena

last: Topouzi

address: Royal School of Mines, Imperial College, Prince Consort Road

country: United Kingdom

institute: Imperial College London

description: Gene expression data from keratinocytes after incubation with Epilife

hyb_protocol: The cRNA was then transferred for hybridization and scanning onto the GeneChip™ Human Genome U133 Plus 2.0 Array.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
Raw data from the microarray was analysed using the commercial software package GeneSpring GX 14.9 (Agilent Technologies Inc.). The intensity values of the samples were normalised and summarised using RMA algorithm.
The intensity values of the samples were normalised and summarised using RMA algorithm.

label_protocol: RNA was used to synthesize first-strand complementary DNA (cDNA) using Nugen Ovation V2. This was then converted to double-stranded cDNA, and used as a template for in vitro transcription to generate cRNA using the Nugen Encore Biotin Module.

growth_protocol: Keratinocytes were seeded at a density of 6000 cells/cm2 using Epilife supplemented with EDGS.

extract_protocol: After 6 hours, media was removed, cells were washed in PBS, then RNA was collected using the RNeasy Plus Micro Kit (Qiagen).

treatment_protocol: Conditioned media obtained from DPFi, sAXL, and control with just Epilife supplemented with EDGS were added on the wounded cells.

value: primary cell line

value: keratinocytes

tag: treatment

value: Epilife


title: C6 undifferentiated

tag: passage number


title: Bone marrow stromal cells, S5544

tag: donor

value: d (IDDM)


title: AG1296-1uM-treated rep1

description:
AG1296_1M_Rep1
Gene expression data from cCFU-Fs treated with 1uM AG1296

source_name: cCFU-F_AG1296 treated with 1uM

value: 12 weeks

tag: Sex

value: male

value: cardiac colony forming units - fibroblast (cCFU-F)

tag: isolated cardiac cells

value: SCA1+PDGFRα+CD31- (S+P+)

tag: treated with


title: Keratinocytes incubated with DPFi_CM, biological replicate 2

description: Gene expression data from keratinocytes after incubation with DPFi CM


title: Bone marrow stromal cells, S5537

tag: gender

value: M

tag: diabetes

value: h

tag: passage

tag: stimulation

value: REST

value: bone marrow-derived stromal cells (BMSC)


title: Bone marrow stromal cells, S5680

tag: age


title: iWAT sample.hfd_ko4

tag: diet/treatment

value: High Fat Diet

tag: genotype

value: FMRKO (AdipoqCre+, MRflox/flox )

tag: tissue

value: inguinal white adipose tissue


title: iWAT sample.hfd_ko3


title: iWAT sample.cort_con1

value: Corticosterone

value: control (MRflox/flox )


title: OCI-LY-10-B

description: Gene expression Parental

source_name: cell line parental rep 2

tag: cell type

value: ABC-DLBCL

tag: drug (ibrutinib) sensitivity

value: Sensitive


title: iWAT sample.hfd_ko2


title: Bone marrow stromal cells, S5536

value: F

value: d (NIDDM)


title: iWAT sample.cort_con2


title: Bone marrow stromal cells, S5676


title: Keratinocytes incubated with sAXL, biological replicate 2

description: Gene expression data from keratinocytes after incubation with sAXL

value: primary cell line

value: keratinocytes

value: sAXL


title: AG1296-1uM-treated rep2

description:
AG1296_1M_Rep2
Gene expression data from cCFU-Fs treated with 1uM AG1296

tag: strain

value: 12 weeks

value: male

value: cardiac colony forming units - fibroblast (cCFU-F)

value: SCA1+PDGFRα+CD31- (S+P+)


title: iWAT sample.cort_con3


title: iWAT sample.cort_con4


title: Bone marrow stromal cells, S5538

value: M

value: h

value: REST

value: bone marrow-derived stromal cells (BMSC)


title: iWAT sample.cort_ko1

value: Corticosterone

value: FMRKO (AdipoqCre+, MRflox/flox )

value: inguinal white adipose tissue


title: Bone marrow stromal cells, S5531


title: Bone marrow stromal cells, S5532


title: iWAT sample.cort_ko2


title: Bone marrow stromal cells, S5535


title: Bone marrow stromal cells, S5675


title: iWAT sample.cort_ko3


title: Bone marrow stromal cells, S5530


title: iWAT sample.hfd_ko1

value: High Fat Diet


title: Keratinocytes incubated with Epilife, biological replicate 1

tag: treatment

value: Epilife


title: Bone marrow stromal cells, S5674


title: iWAT sample.1_chow_con1

value: Chow

value: control (MRflox/flox )


title: Bone marrow stromal cells, S5679

value: F

value: d (NIDDM)


title: iWAT sample.cort_ko4


title: Bone marrow stromal cells, S5673


title: iWAT sample.4_chow_con4


title: iWAT sample.2_chow_con2


title: iWAT sample.5_chow_con5


title: Bone marrow stromal cells, S5678


title: Bone marrow stromal cells, S5534


title: iWAT sample.6_chow_ko1


title: Bone marrow stromal cells, S5533


title: iWAT sample.7_chow_ko2


title: Bone marrow stromal cells, S5543


title: Bone marrow stromal cells, S5542


title: Bone marrow stromal cells, S5539


title: iWAT sample.10_chow_ko5


title: WH008

city: Munich

first: Hans

middle: Carlo

last: Maurer

state: Bavaria

address: Ismaninger Str. 22

department: II. Medizinische Klinik

institute: Klinikum rechts der Isar

data_processing:
RTA (Illumina) was used for base calling and
bcl2fastq (version 2.20) was used to convert BCL to fastq format, coupled with adaptor trimming.
Pseudoalignment was carried out to a kallisto index created from the murine GRCm38 transcriptome using kallisto (0.44.0) and
estimated counts and transcripts per kilobase million (TPM) per gene were computed from the kallisto output using the tximport R package.
Genome_build: Mouse GRCm38
Supplementary_files_format_and_content: tab-delimited text file containing raw read count values per gene for each sample

extract_protocol:
Qiagen RNAeasy Plus Micro Kit
Clontech Ultra Low v4 kit to amplify total RNA. Nextera XT protocol using the resulting cDNA for library preparation.

value: sham


title: WH007


title: Bone marrow stromal cells, S5677


title: Keratinocytes incubated with sAXL, biological replicate 1

value: primary cell line

value: keratinocytes

value: sAXL


title: WH006


title: Bone marrow stromal cells, S5541


title: OCI-LY-10-A

description: Gene expression Parental

tag: cell line

value: ABC-DLBCL

value: Sensitive


title: WH005


title: Bone marrow stromal cells, S5529

tag: donor

value: M

value: h

value: REST


title: Bone marrow stromal cells, S5540

value: bone marrow-derived stromal cells (BMSC)


title: WH004

value: scopolamine


title: WH003


title: miR142-WT-4

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

hyb_protocol: 2 µg of the labeled cDNA were hybridized for 22h at 65°C in Agilent hybridization chambers. The cDNA was not fragmented before hybridization.

scan_protocol: The dried slides were scanned at 2 µm/pixel resolution using the InnoScan is900 (Innopsys, Carbonne, France).

data_processing: Image analysis was performed with Mapix 6.5.0 software, and calculated values for all spots were saved as GenePix results files. Mean spot signals were quantile normalized.

source_name: primary isolated alveolar type-II cells

label_protocol: Purified total RNA was amplified using the Ovation PicoSL WTA System V2 kit (NuGEN Technologies, Bemmel, Netherlands). Per sample, 2µg amplified cDNA was Cy-labeled using the SureTag DNA labeling kit (Agilent, Waldbronn, Germany).

growth_protocol: Mothers were grown under standard conditions. Embryonic lungs at E18.5 were isolated and sorted for AEC II cells using FACS sorter and then RNA was isolated.

extract_protocol: Qiagen miRNeasy mini kit

value: Bl/6 R26-miR-142Sftpc-CreERT2/+

value: primary isolated alveolar type-II cells

value: wild type


title: Keratinocytes incubated with DPFi_CM, biological replicate 1


title: WH002


title: NHKC SLS Treated 1: Human epimermal keratinocytes, 10 microM SLS treated, biological replicate 1

city: Seoul

first: Minsoo

last: Noh

address: 1 Gwanak-ro, Gwanak-gu

department: Pharmacy

country: South Korea

institute: Seoul National University

description: Gene expression data from 10 microM SLS treated-cultured human epidermal primary keratinocytes for 24 hours

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 oligonucleotide arrays. GeneChips were hybridized and washed using the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using a Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Affymetrix Expression Console software using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Cultured human primary epidermal keratinocytes, 10 microM SLS treated for 24 hours

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 6 μg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Normal human epidermal keratinocytes (NHKCs) from neonatal foreskin were purchased from Lonza (Basel, Switzerland) and cultured in KBM medium with KGM2 growth supplements according to the manufacturer's instuction

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: At passge 2, when NHKCs were confluent in culture,10 microM SLS or 1 microM urushiol was treated. After 24 hours in culture, NHKCs were harvested for total RNA isolation.

value: human epidermal keratinocytes (primary cell culture, passage 2)


title: miR142-WT-3


title: iWAT sample.8_chow_ko3

value: Chow

value: FMRKO (AdipoqCre+, MRflox/flox )

value: inguinal white adipose tissue


title: WH001


title: NHKC Urushiol Treated 2: Human epimermal keratinocytes, 1 microM urushiol treated, biological replicate 2

description: Gene expression data from 1 microM urushiol treated-cultured human epidermal primary keratinocytes for 24 hours

source_name: Cultured human primary epidermal keratinocytes, 1 microM urushiol treated for 24 hours


title: Papillary thyroid cancer 2

type: genomic

city: Ulm

first: Rabea

last: Wagener

address: Albert-Einstein-Allee 11

department: Ulm University and Ulm University Medical Center

institute: Institute of Human Genetics

description: Hypridized to OncoScan CNV array

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner.

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Data were normalized using the OncoScan Console 1.3 and viewed using Nexus for OncoScan.

molecule: genomic DNA

source_name: Patient with FvPTC-T2

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from i) mononuclear cell from  peripheral blood and fresh frozen papillary thyroid tumors using the DNeasy Blood and Tissue kit (Qiagen) or ii) macrodisected sections of formaline fixed paraffine embedded tissue from multinodular goitre specimens usign the Maxwell RSC FFPE DNA kit from Promega.

tag: tissue type

value: papillary thyroid cancer

tag: conservation method

value: Cryo


title: shATF1 infected hESCs rep2

city: Taipei

first: Shang-Chih

last: Yang

address: 128 Academia Road, Section 2, Nankang, Taipei, 115, Taiwan

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

description: Gene expression data from shATF1 hESCs

hyb_protocol: After aRNA fragmentation, 12.5 ug of fragmented aRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array. Affymetrix Fluidics Station 450 was used for gene chips washing and staining.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and use Gene Spring Software 12 to normalize data (RMA mode).

source_name: shATF1 (TRCN0000273834) infected hESCs for 6 days rep2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA (GeneChip® 3’ IVT Express Kit, Affymetrix).

growth_protocol: hESCs were cultured in Dulbecco’s modified Eagle’s medium (DMEM)/F12 supplemented with 20% knockout serum replacement, 2 mM L-glutamine, 1% nonessential amino acids, 8 ng/mL human bFGF, and 0.1 mM 2-mercaptoethanol.

treatment_protocol: 1.5 x 10^5 cells of hESCs were seeded (per well of 6 well plate), and later incubated with the supernatants containing lentivirus (lentivirus multiplicity of infection (MOI) = 10). hESCs were cultured with MEF conditioned medium for 16 hours with protamine sulfate (8 ug/mL). Then the hESCs were selected with 2ug/mL puromycin for 6 days

value: Human embryonic stem cells (hESCs)


title: NHKC SLS Treated 2: Human epimermal keratinocytes, 10 microM SLS treated, biological replicate 2


title: shATF1 infected hESCs rep1

description: Gene expression data from shATF1 hESCs

scan_protocol: GeneChip® Human Genome U133 Plus 2.0 Array

source_name: shATF1 (TRCN0000273833) infected hESCs for 6 days rep1


title: ko4

growth_protocol: Mothers were grown under standard conditions.

tag: genotype/variation

value: mir142 knock-out


title: Papillary thyroid cancer 1

description: Hypridized to OncoScan CNV array

source_name: Patient with FvPTC-T1


title: OsINO1 introgressed  no salt treated line set-2 (control)

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression under no salt condition from total  leaf RNA

hyb_protocol: Labeled cRNA sample were fragmented at 60ºC and hybridized on to Agilent  Rice Gene Expression  8x60k Array (AMADID: 031380) by Genotypic Technology Private Limited. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2505C).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the percentile shift method.

source_name: rice leaf sample_OsINO1_no salt

label_protocol: The samples for gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasyMini kit columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Seeds of One month old plant lines (Os/Pc) were germinated in Murashige and Skoog medium (1962) for 15 days and thereafter kept in soil rite

extract_protocol: Total RNA was extracted from rice leaves of the plant lines (Os/Pc) using RNA isolation kit from Bioline

treatment_protocol: One month old plant lines (Os/Pc) , kept in soil rite and treated with 150mM NaCl  for 5 days.

value: Whole leaf tissue

tag: cultivar


title: OsINO1 introgressed salt treated line set-3(biological replicate)

description: Gene expression after five days of salt stress in 150mM NaCl from total  leaf RNA

source_name: rice leaf sample_OsINO1_salt treated


title: miR142-OE-4

value: tamoxifen (0.1mg/g) at E14.5

value: mir142 overexpressing


title: PcINO1 introgressed salt treated line set-3 (biological replicate)

source_name: rice leaf sample_PcINO1 _salt treated


title: NHKC Control 2: Human epimermal keratinocytes, vehicle treated, biological replicate 2

description: Gene expression data from vehicle treated-cultured human epidermal primary keratinocytes for 24 hours

source_name: Cultured human primary epidermal keratinocytes, vehicle treated for 24 hours


title: NHKC Control 1: Human epimermal keratinocytes, vehicle treated, biological replicate 1


title: miR142-WT-2


title: NHKC Urushiol Treated 1: Human epimermal keratinocytes, 1 microM urushiol treated, biological replicate 1


title: shRFP infected hESCs rep2

description: Gene expression data from shRFP hESCs

source_name: shRFP (TRCN000007220) infected hESCs for 6 days rep2


title: miR142-OE-2


title: miR142-WT-1


title: miR142-OE-1


title: Multinodular goiter 3

description: Hypridized to OncoScan CNV array

source_name: Patient III-2 MNG tumor

value: multinodular goiter

value: FFPE


title: PcINO1 introgressed salt treated line set-1


title: ko2


title: PcINO1 introgressed salt treated line set-2 (biological replicate)


title: miR142-OE-3


title: Multinodular goiter 2

description: Hypridized to OncoScan CNV array

source_name: Patient III-3 MNG tumor


title: Multinodular goiter 1

description: Hypridized to OncoScan CNV array

source_name: Patient III-1 MNG tumor


title: Germline sample

description: Hypridized to OncoScan CNV array

source_name: Patient III-1 germline

value: Blood


title: ko1


title: ko3


title: shRFP infected hESCs rep1

description: Gene expression data from shRFP hESCs

source_name: shRFP (TRCN000007220) infected hESCs for 6 days rep1


title: wt4

source_name: primary isolated alveolar type-II cells


title: HCT116 wt biological replicate 3

city: Salamanca

first: Javier

last: De Las Rivas

address: Campus Miguel de Unamuno

department: CSIC and University of Salamanca

country: Spain

institute: Cancer Research Center (CiC-IBMCC)

description: cell line: HCT116 wt biological replicate 3 tissue: colorectal carcinoma

hyb_protocol: The Nanostring hybridization reaction containing 3 µl Reporter CodeSet, 5 µl hybridization buffer, 2 µl Capture ProbeSet and 5 µl total RNA (100 ng) was conducted for 16 h at 65°C. After hybridization, labelled RNA was processed automatedly according to the manufacturer's instructions for approximately 2.5 to 3 h through the NanoString nCounter Prep Station, where mRNA specific magnetic beads separation and mRNA immobilization on the cartridge surface takes place.

scan_protocol: Automated counting and tabulating of signals of the reporter probes was performed using the nCounter Digital Analyzer (Nanostring), a multi-channel epifluorescence scanner specifically configured for use with Nanostring's nCounter cartridges, and standard settings.

data_processing: Data were processed internally using the nCounter Digital Analyzer (Nanostring). The number of mRNA specific reporter signals counted corresponds to number of respective mRNA molecules counted and present in the sample. For each sample, one Reported Code Count (RCC) file is generated, which contains the gene expression raw data. RCC files were downloaded from the nCounter Digital Analyzer and imported into the nSolver Analysis Software 3.0 (Nanostring) for data processing, quality control and analysis. Finally, housekeeping gene (geometric mean of 40 genes) normalization for quantitating gene expression levels, positive control normalization for background noise correction and data analysis was performed using nSolver™ Analysis Software 3.0 (NanoString Technologies, Hamburg, Germany) and standard settings. The fold-change of counts was determined by averaging results per p21 ko cell line and comparing them to average counts of HCT116 cells. Matrix tables contain normalized counts, raw data and fold change (FC) data of six samples (see samples list above) obtained from the nSolver Analysis Software 3.0. Fold changes of counts were determined by averaging results per p21 ko cell line (n = 1-3) and by comparing them to the average counts of HCT116 cell line (n = 3) and are given in excel sheet Grouped FC all ko biological replicates.

label_protocol: 100 ng (contaied in 5 µl) of total RNA per sample was labeled with the Reporter CodeSet & Capture ProbeSet included in the following kit: XT_PGX_HuV1_CancerProg_CSO XT-CSO-PROG1-12(Cat. no. 115000152, Nanostring).

growth_protocol: All cell lines HCT116 and p21-/- ko clones cultured in a 100 cm cell culture dish and maintained in RPMI medium supplemented with 1% penicillin/streptomycin and 10% FBS.

extract_protocol: Cell harvesting was performed on ice. Cells were scraped off from the cell culture plates and cell pellets were prepared by centrifugation at 5000 rpm fr 5 min at 4 °C. Cells were washed with PBS, centrifugation was repeated, supernatants were discarded and dry cell pellets were frozen in liquid nitrogen and stred at -80°C. RNA was isolated from frozen cell pellets using the QIAzol Lysis Reagent (Qiagen) and RNeasy Mini Kit (Qiagen) according to the manufacturer's protocols.

treatment_protocol: No treatment was applied.

value: colorectal carcinoma

value: wt


title: HCT116 p21 -/- biological replicate 1

description: cell line: HCT116 p21 -/- biological replicate 1 tissue: colorectal carcinoma


title: HCT116 p21 -/-  biological replicate 2

description: cell line: HCT116 p21 -/- biological replicate 2 tissue: colorectal carcinoma


title: HCT116 p21 -/-  biological replicate 3

description: cell line: HCT116 p21 -/- biological replicate 3 tissue: colorectal carcinoma


title: wt2

value: wild type


title: wt1


title: wt3


title: HCT116 wt biological replicate 1

description: cell line: HCT116 wt biological replicate 1 tissue: colorectal carcinoma


title: OsINO1 introgressed salt treated line set-2 (biological replicate)


title: OsINO1 introgressed  no salt treated line set-1 (control)


title: fetal biceps_cortisol_140d_ replicate 6

city: Gainesville

first: Maureen

last: Keller-Wood

state: Florida

address: 1225 Center Dr

department: Pharmacodynamics

institute: University of Florida

description: Gene expression at 140 days gestation in fetal biceps femoris

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.3 pmol Cy3/µg cRNA) was  fragmented and hybridized to Agilent Sheep Oligo Microarrays (G4813A) by the ICBR facility at the University of Florida according to Agilent's methodology.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color (green) scan setting for 8x15k array slides, by the ICBR facility at University of Florida.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1.1.1 (Agilent) using default parameters (protocol GE1-v5_10 and Grid: 019921_D_F_20100112)  background detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were normalized to the chip median and log transformed.

organism: Ovis aries

source_name: fetal biceps_cortisol_140d_ replicate 6

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA using the One-Color Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Continuous infusions of cortisol to the ewe were begun at approximately day 115 of gestation

extract_protocol: RNA was extracted with Trizol (Life Technologies, Carlsbad, CA), and purified through Qiagen Rneasy+ kits with on-column DNase digestion (QIAGEN, Valencia, CA) according to manufacturers' protocols.Total RNA concentration was measured by Nanodrop ND-1000 and RNA quality was monitored by Agilent Bioanalyzer

treatment_protocol: Ewes were infused with 1mg/kg/day cortisol or vehicle from approximately day 115 to 140 d of pregnancy (n=7, cortisol; n=7 control). Fetal Samples of left ventriclar free wall (n=5 control, n=5 cortisol) were then collected and RNA extracted.

value: fetal biceps femoris

tag: treatment group

value: cortisol 140d gestation


title: OsINO1 introgressed salt treated line set-1


title: fetal biceps_cortisol_140d_ replicate 3

source_name: fetal biceps_cortisol_140d_ replicate 3


title: rlt1/2-rep2

city: Beijing

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using HISAT-2.1.0 with default parameters
High-throughput sequencing reads were normalized by edgeR TMM algorithm.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include normalized expression values for each Sample

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown on MS medium plates with 16 h of light at 23 ºC and 8 h of darkness at 21 ºC.

extract_protocol:
10-day-old Arabidopsis seedling were collected for RNA extraction. Total RNA was extracted by Trizol
libraries were prepared for mRNA-seq

tag: seedlings

value: Arabidopsis seedlings

tag: genetype

tag: ecotype


title: rlt1/2-rep1


title: fetal biceps_cortisol_140d_ replicate 5

source_name: fetal biceps_cortisol_140d_ replicate 5


title: HCT116 wt biological replicate 2

description: cell line: HCT116 wt biological replicate 2 tissue: colorectal carcinoma


title: chr11/17-rep2


title: arid5-rep2


title: chr11/17-rep1


title: fetal biceps_cortisol_140d_ replicate 2

source_name: fetal biceps_cortisol_140d_ replicate 2


title: Pi_tZ_R1

city: Pozuelo de Alracon

first: Juan

middle: Carlos

last: del Pozo

state: Madrid

address: Campus de Montegancedo, UPM

department: Biotechnology

institute: Centro de Biotecnología y Genómica de Plantas

description: grown with phosphate and treated with trans-zeatin

data_processing:
Basecalls performed using CASAVA version 1.4
Clean (FastQC software (Babraham-Bioinformatics, 2014).  Reads are mapped to a reference sequences using HISAT2 with 8 mismatches allowed.
Reads count to a reference  genome  (TAIR 42.gff3) using the htseq-count tool.
Differential expression analysis was calculated with edgeR with the following parameters: FDR<0.05, fold change >2 fold  or   < -2 fold
Genome_build: Atabidopsis thaliannTAIR 10
Supplementary_files_format_and_content: tab-delimited text files including normalized counts.

source_name: roots

growth_protocol: Arabidopsis thalinaan (Col-0) seedlings were grown  in Murashige and Skoog medium containing 625 or 5 µM of phosphate for 8 days  and then treated with 5 µM of cis-zeatin or trans-zeatin fro 8 hours.

extract_protocol:
Total  RNA was isolated from Arabidopsis plants using the Trizol reagent and RNeasy columns (Qiagen). Quantity and quality measurements were taken using a NanoDrop spectrophotometer and Bioanalyzer.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized  using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short  fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent  2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using  Illumina HiSeqTM 2000 or other sequencer when necessary
polyA library

value: Columbia


title: arid5-rep1


title: fetal biceps_control_140d_ replicate 6

source_name: fetal biceps_control_140d_ replicate 6

value: control 140d gestation


title: fetal biceps_control_140d_ replicate 3

source_name: fetal biceps_control_140d_ replicate 3


title: fetal biceps_cortisol_140d_ replicate 1

source_name: fetal biceps_cortisol_140d_ replicate 1


title: fetal biceps_control_140d_ replicate 5

source_name: fetal biceps_control_140d_ replicate 5


title: fetal biceps_control_140d_ replicate 4

source_name: fetal biceps_control_140d_ replicate 4


title: fetal biceps_control_140d_ replicate 1

source_name: fetal biceps_control_140d_ replicate 1


title: fetal biceps_control_140d_ replicate 2

source_name: fetal biceps_control_140d_ replicate 2


title: fetal biceps_cortisol_140d_ replicate 4

source_name: fetal biceps_cortisol_140d_ replicate 4


title: WT-rep2

description: arid5_normalize.txt; chr1117_normalize.txt; rlt12_normalize.txt


title: WT-rep1


title: ARID5-GFP-rep2

description: DNA extracted by antibody

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were aligned to the TAIR10 genome assembly using bowtie2 version 2.2.6 with parameters -k 1 -N 1 -p 20 --local -q
peaks were called using macs2 version 2.1.1.20160309 with the following setting: macs2 callpeak -f  BAM  -g 1.2e8  --bdg --nolambda
Genome_build: TAIR10
Supplementary_files_format_and_content: bw files were generated using deeptools bamCoverage with parameters --binSize 10 -p 30 --normalizeUsing RPKM --outFileFormat bigwig

extract_protocol:
A 2-g quantity of 10-day-old Arabidopsis seedlings was ground into powder and cross-linked with 1% formaldehyde (Sigma, F8775) in 15 ml of lysis buffer (20 mM Tris-HCl, pH 7.5, 20 mM KCl, 2 mM EDTA, pH 8.0, 2.5 mM MgCl2, 25% glycerol, 250 mM sucrose, 5 mM DTT, 0.1 mM PMSF, and Roche protease inhibitor cocktail) for 20 min at 4 °C.
libraries were prepared for ChIP-seq

tag: seedling

tag: antibody


title: fetal left ventricle_cortisol_140d_ replicate 5

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.5 pmol Cy3/µg cRNA) was  fragmented and hybridized to Agilent Sheep Oligo Microarrays (G4813A) by the ICBR facility at the University of Florida according to Agilent's methodology.

source_name: fetal left ventricle, term,  cortisol, replicate 5

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low Input Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

tag: tissue

value: fetal left ventricle

value: cortisol


title: Col-0-GFP-rep1

description: DNA extracted by antibody

tag: genotype

value: wildtype


title: Col-0-GFP-rep2

description: DNA extracted by antibody


title: fetal left ventricle_cortisol_140d_ replicate 4

source_name: fetal left ventricle, term,  cortisol, replicate 4


title: fetal left ventricle_cortisol_140d_ replicate 3

source_name: fetal left ventricle, term,  cortisol, replicate 3


title: fetal left ventricle_cortisol_140d_ replicate 2

source_name: fetal left ventricle, term,  cortisol, replicate 2


title: Col_ser5_1

first: Jincong

last: Zhou

address: Tsinghua Yuan

institute: Tsinghua University

data_processing:
R2 of paired-end reads were trimmed for Illumina adaptors and then the reads <10bp were filtered by using the Cutadapt (v1.9.1).
Filtered R2 reads were aligned to the Arabidopsis reference genome (TAIR10) using Bowtie 2 version 2.3.0 with default settings.
BAM files were converted to bigWig using RPGC normalization method in deeptools v2.26.0.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage with binSize 1bp.

growth_protocol: 14-day seedlings growth on 1/2 MS media.

extract_protocol:
14-day old seedlings were harvested from 1/2MS media and were grounded in liquid nitrogen and resuspended in ice-cold lysis buffer (50mM HEPES pH 7.5, 150mM NaCl, 1mM EDTA pH 8.0, 1% Triton X-100, 10% glycerol, 5mM β-mercaptoethanol, 1mM PMSF, 2μg/μl Aprotinin and 2μg/μl Pepstatin A) for 30 mins on ice. After lysis mixture was filtered and centrifuged to discard the supernatant, Nuclear pellet was washed once with ice-cold HBB (25mM Tris-HCl pH7.6, 0.44M sucrose, 10mM MgCl2, 0.10% Triton-100, 10mM β-mercaptoethanol) and HBC (20mM Tris-HCl pH7.6, 0.352M sucrose, 8mM MgCl2, 0.08% Triton-100, 8mM β-mercaptoethanol and 20% glycerol) buffers, respectively. Washed nuclear pellet was resuspended in MNase reaction buffer (20mM Tris-HCl pH 8.0 , 5mM NaCl, and 2.5mM CaCl2, 20U MNase (TAKARA)). The reaction mixture was incubated at 37°C for 5 minutes and the reaction was later stopped with final con. 0.02M EDTA. Then sonication was performed 1s ON/OFF for 10 cycles to release chromatin and centrifuged to obtain the supernatant. The collected supernatant was diluted 5-8 times with ice-cold NET-2 buffer (50mM Tris-HCl pH7.4, 150mM NaCl, and 0.05% NP-40). The diluted supernatant was incubated with Pol II Ser5p antibody (MBL Life science, MABI0603) coated Dynabeads (Invitrogen, 11201D) for 2 hours at 4°C and the beads containing complex was washed 8 times with ice-cold NET-2 buffer. Finally, beads were resuspended with PNK reaction mixture containing 75 μl PNK buffer, 10 μl PNK enzymes (NEB) and 15 μl of 10mM ATP and incubated at 37°C for 10 mins on a Thermomixture (1400 rpm). After that supernatant was removed and beads were washed once with NET-2 buffer. Then beads was followed RNA extraction with Trizol reagent. The extracted RNA was performed gel size selection with 8% PAGE gel and the gel corresponding to 35-100bp size of RNA was collected and recovered from gels.
The recovered RNA was used to construct the small RNA libraries with NEXTflex TM small RNA-Seq Kit V3. Finally, the libraries were recovered from the 6% PAGE gel corresponding to 140-250 bp size and undergone high throughput deep sequencing.

tag: ecotype background

tag: development stage

value: 14-day seedlings

tag: ssdrip antibody

tag: molecule subtype

value: nuclear RNA


title: fetal left ventricle_control_140d_ replicate 5

source_name: fetal left ventricle, term, no cortisol, replicate 5

value: control


title: Col_ser5_2

value: Pol II Ser5p antibody (MBL Life science, MABI0603)


title: nrpe1_ser5_1


title: fetal left ventricle_control_140d_ replicate 1

description: Gene expression at 140 days gestation in left ventricle

source_name: fetal left ventricle, term, no cortisol, replicate 1


title: fetal left ventricle_control_140d_ replicate 3

source_name: fetal left ventricle, term, no cortisol, replicate 3


title: H-NS (ΔluxR) [GSF2140-Delta-luxR-1_S86]

city: Bloomington

first: Julia

middle: C

last: van Kessel

state: IN

address: 1001 E 3rd Street

department: Biology

institute: Indiana University

data_processing:
Read sequences were de-multiplexed using bcl2fastq (software versions 2.1.0.31).
Sequencing reads were trimmed for quality and adapters using Trimmomatic (v0.33 for all samples except the DluxR ChIP H-NS samples which used v0.38) with the following parameters: ILLUMINACLIP:adapters.fa:3:20:6 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:30
Reads were mapped to the genome using bwa (v0.7.17).
Read counts were determined for genes and intergenic regions using a custom perl script
Genome_build: Vibrio harveyi ATCC BAA-1116 with the refseq IDs NC_009783.1, NC_009784.1, and NC_009777.1
Supplementary_files_format_and_content: countstable has read counts for genes and intergenic regions of the genome

organism: Vibrio campbellii

source_name: ΔluxR Δhns (RRC169)

growth_protocol: Cells were grown at 30 °C to an OD600 of 1.0

extract_protocol:
RNA was extracted using Trizol and chloroform
For GSF1906 samples, total RNA was first treated with Ribo-Zero rRNA Removal Kit (Bacteria) (Illumina, cat#MRZMB126) to remove excess ribosomal RNA
For GSF2140 samples, total RNA was first treated with RiboMinus Transcriptome Isolation Kit (Bacteria) (ThermoFisher Scientific, cat#K155004) to remove excess ribosomal RNA
All libraries were prepared using ScriptSeq RNA-Seq Library Preparation kit (Illumina, cat#SSV21124) according to manufacturer’s protocol
For all samples, sequencing barcodes selected from TruSeq Dual Index Sequencing Primer Box, Paired-End (Illumina cat#PE-121-1003) were added to the libraries during construction for multiplexing. The barcoded libraries were cleaned with AMPure XP beads (Beckman Coulter, cat#A63882), verified using Qubit3 fluorometer (ThermoFisher Scientific) and 2200 TapeStation bioanalyzer (Agilent Technologies), then pooled
Pooled libraries were sequenced on Illumina NextSeq 500 (Illumina) with NextSeq75 High Output v2 kit (Illumina cat#FC-404-2005)
The GSF1906 libraries were sequenced on single-end 75 bp run
The GSF2140 libraries were sequenced on paired-end 2x38 bp run

tag: strain background

value: ATCC BAA-11116

value: {delta}luxR {delta}hns (RRC169)

tag: sample type

value: Bacterial lysate


title: ARID5-GFP-rep1

description: DNA extracted by antibody

source_name: Arabidopsis seedlings


title: nrpe1_ser5_2


title: fetal left ventricle_control_140d_ replicate 2

source_name: fetal left ventricle, term, no cortisol, replicate 2


title: H-NS (ΔluxR) [GSF2140-Delta-luxR-2_S87]


title: H-NS [GSF2140-Delta-hns-Delta-luxR-2_S96]

source_name: Δhns (RRC049)

value: {delta}hns (RRC049)


title: fetal left ventricle_control_140d_ replicate 4

source_name: fetal left ventricle, term, no cortisol, replicate 4


title: H-NS (ΔluxR) [GSF2140-Delta-luxR-3_S88]


title: WT_Al

city: Hangzhou

first: Zhong Jie

last: Ding

address: 866# Yuhangtang Rd

institute: Zhejiang University

hyb_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols

scan_protocol: The arrays were scanned by the Affymetrix Scanner 3000(Affymetrix)

data_processing: Affymetrix GeneChip Command Console (version 4.0, Affymetrix) was used to analyze array images to get raw data. MAS5.0 was used for normalization.

source_name: root sample_wildtype_Al

growth_protocol: 4-week-old plants grown under hydroponic culture.

extract_protocol: Total RNAs were isolated using the RNase kit (Qiagen)

treatment_protocol: Plants were transferred to with 0.5 mM CaCl2 solution with or without 25µM AlCl3 for 6 hours

value: root

tag: age

value: 4 weeks


title: H-NS [GSF2140-Delta-hns-Delta-luxR-3_S97]


title: H-NS [GSF2140-Delta-hns-Delta-luxR-1_S95]


title: ∆Ms_1939_3

city: chongqing

first: jingjing

last: niu

institute: Southwest University

data_processing:
Sequenced reads were filtered for Seqtk, and get clean Reads that can be used for data analysis, using the bowtie2 (version: 2-2.0.5), the Genome mapping was performed on post-pretreatment reads, which was more suitable for the sequencing data of the prokaryotic transcriptome. The comparison result generated by Mapping is the BAM file
Fragments Per Kilobase of exon model per Million mapped reads.We first apply HTSeq in TopHat than after each gene Fragments could count to count, and then use TMM (trimmed mean of M values) normalization method, finally calculated using perl script FPKM value of each gene.
Genome_build: Mycobacterium smegmatis MC2 155 uid57701
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Mycolicibacterium smegmatis MC2 155

growth_protocol: WT, ∆MS_1939, strains were grown in Middlebrook 7H9 broth in 250ml bottles (supplemented with 0.05% Tween80 and 1% acetamide) .

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Paired-end libraries were synthesized by using the TruSeq® RNA Sample Preparation Kit (Illumina, USA) following TruSeq® RNA Sample Preparation Guide.
The cDNA fragments afterwards through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.

treatment_protocol: When WT and ∆MS_1939  strains were grown until OD600 =0.8, add Rif to final concentration of 40μg/mL, 24 h induction.

tag: genotype/variation

value: m4C methyltransferase Ms_1939 deletion mutant


title: wrky47_Al

source_name: root sample_wrky47_al

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols


title: U251MG NSC p13 0.37EPZ015666

city: Durham

first: Landon

middle: J

last: Hansen

state: NC

address: 203 Research Drive, MSRB1 Rm 171

institute: Duke University School of Medicine

scan_protocol: Followed the manufacturer's (Illumina) specifications on an iScan

data_processing: Data were interpreted in GenomeStudio v2011.1 Methylation Module 1.9.0 and exported for analysis

label: biotin nucleotide or dinitrophenyl labeled

source_name: Commercial GBM

label_protocol: A single nucleotide extension was labeled either with biotin or dinitrophenyl according to the manufacturer's (Illumina) specifications

growth_protocol: Cells were cultured in StemCell serum-free media on laminin-coated plates

extract_protocol: Genomic DNA was extracted using the QIAamp DNA Mini Kit (QIAGEN, Cat#51306). Extracted DNA was bisulfite treated with the Zymo bisulfite kit according the manufacturer's specifications

treatment_protocol:
MTDIA was added to indicated sample 7 days after transduction with OMRP transformation factors
EPZ015666 was added to culture media at indicated concentration and samples were cultured for 30 days.

tag: gender

value: Male

tag: mtap

value: MTAP expressed (PRMT5 inhibited)


title: ∆Ms_1939_2


title: NHA OMRP-6 CRISPR MTAP -/-

hyb_protocol: Followed the manufacturer's (Illumina) specifications

source_name: Transformed Commercial Astrocytes

value: MTAP deleted


title: LuxR [GSF1906-Delta-hns-3_S66]

source_name: ΔluxR (KM669)

value: {delta}luxR (KM669)


title: ∆Ms_1939_1


title: NHA OMRP-6 NTC

value: MTAP Expressed


title: WT_CK

source_name: root sample_wildtype_control

value: wildtype


title: WT3

source_name: WT

value: wild type


title: LuxR [GSF1906-Delta-hns-2_S65]


title: wrky47_CK

source_name: root sample_wrky47_control


title: LuxR [GSF1906-Delta-hns-1_S64]


title: NHA OMRP-1 3uM MTDIA

value: MTAP inhibited


title: WT1


title: WT [GSF1906-Delta-BB120-3_S69]


title: U251MG NSCp13

value: MTAP expressed


title: Zinc_3

city: North Ryde

first: Varsha

last: Naidu

address: 14 Eastern Rd

department: Molecular Sciences

institute: Macquarie University

data_processing:
Basecalling and adaptor sequence trimming were processed by commercial sequencing provider
The sequence reads from 6 samples were analysed using EDGE-pro (Estimated Degree of Gene Expression in Prokaryotic Genomes), where reads were aligned to the A. baumannii AB5075 reference genome (Genbank accession: CP008706.1).
Raw counts (not RPKM values) were used to generate genes with differential expression using the R package DESeq2
Genome_build: A. baumannii AB5075 reference genome (Genbank accession: CP008706.1)

organism: Acinetobacter baumannii

source_name: Bacterial planktonic cells grown in Müller Hinton broth

growth_protocol: Three independent A. baumannii AB5075-UW cultures were grown overnight in 5ml of Muller-Hinton (MH, Oxoid) broth with shaking (200rpm) at 37°C. The overnight cultures were diluted 1:100 in MH and grown for ~2h at 37°C to mid-log phase (OD600 of 0.6)

extract_protocol:
RNA extraction was carried out using the miRNeasy mini kit (Qiagen) and DNA was eliminated using the TURBO DNA-free kit (Ambion Inc, USA). The cDNA library was generated using the TruSeq® Stranded Total RNA Sample Preparation kit (Illumina, Inc., USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treatment cultures were treated with 2.5mM ZnSO4 (Sigma-Aldrich)

tag: strain

tag: treatment

value: Treated with 2.5mM ZnSO4


title: Zinc_1


title: HCC827_VECTOR

city: Guangzhou

first: Han

last: Tian

state: Guangdong

address: No.74, Zhongshan Er Road

department: Zhongshan School of Medicine

institute: Sun Yat-sen University

data_processing:
Bustard software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to HG38 whole genome using bowtie2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by using HTseq.
Genome_build: HG38
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each samples were attached.

source_name: HCC827 cell line, NSCLC

extract_protocol:
RNA was harvested using Trizol reagent. RNA was prepared by using Ribo-Zero Magnetic Kit (rRNA-depleted RNA). Illumina TruSeq Stranded mRNA Kit was used  for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: VECTOR


title: WT [GSF1906-Delta-BB120-1_S67]

value: ATCC BAA-11116


title: WT [GSF1906-Delta-BB120-2_S68]

value: Bacterial lysate


title: WT2


title: H-NS_ChIP (ΔluxR)

data_processing:
Read sequences were de-multiplexed using bcl2fastq (software versions 2.1.0.31).
Sequencing reads were trimmed for quality and adapters using Trimmomatic (v0.33 for all samples except the DluxR ChIP H-NS samples which used v0.38) with the following parameters: ILLUMINACLIP:adapters.fa:3:20:6 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:30
Reads were mapped to the genome using bwa (v0.7.17).
Peaks were identified using macs2 (v2.1.2) call peak algorithm.
Genome_build: Vibrio harveyi ATCC BAA-1116 with the refseq IDs NC_009783.1, NC_009784.1, and NC_009777.1
Supplementary_files_format_and_content: Processed data files are tab-delimited files identifying the peaks associated with specific samples with the wild-type ChIP-control as background as specified by the macs2 software.

source_name: Bacterial lysate

extract_protocol:
Cells were lysed using Bugbuster bacterial lysis reagent coupled with sonication
Immunoprecipitated chromatic DNA was subjected to library preparation using NEBNext Ultra II DNA Library kit (NEB cat# E7645S). DNA fragments were end repaired and 5' phosphorylated, and a 3' end Adenosine-tail was added. The products were ligated to a NEB hairpin adapter which contains an uracil at the loop region. The adapter loop was opened by Uracil-Specific Excision Reagent (NEB) to excise the uracil. The products were cleaned with Agencourt AMPure XP beads (Beckman Coulter cat# A63882) but no size selection was applied. 10 (GSF1697) or 12 (GSF2248) PCR cycles were run using 8-nt barcoded oligos from NEBNext Multiplex Oligos barcode kit (NEB cat# 6609S).
Libraries were purified with Agencourt AMPure XP beads, multiplexed and sequenced on NextSeq 500 (Illumina) with NextSeq75 High Output v2.5 kit (Illumina cat# 20024906) to generate paired-end 2x42 bp reads.

treatment_protocol: 1% formaldehyde for 30 minutes at 30 °C

value: deltaluxR

value: FLAG


title: A549_VECTOR

source_name: A549 cell line, NSCLC


title: Mock_ChIP

value: WT


title: fetal left ventricle_cortisol_140d_ replicate 1

source_name: fetal left ventricle, term,  cortisol, replicate 1

value: fetal left ventricle

tag: treatment group

value: cortisol


title: Zinc_2


title: HCC827_AKT1


title: A549_AKT1


title: Wildtype_Input


title: NHA OMRP-1 DMSO Control

value: Male


title: 13-0302 MigR1-MTAP NSC p11

source_name: Patient Derived

value: Female


title: Cell Mix RNA

city: New York

first: Zhu

last: Chenxu

email: cxzhu@pku.edu.cn, czhu@nygenome.org

state: New York

address: 101 Avenue of the Americas

institute: New York Genome Center

data_processing:
Library strategy: Paired-seq
Cellular barcodes and the linker sequences are read by Read2. The first base of BC#1, BC#2, BC#3 and BC#4 should locate within 121-124th, 84-87th, 47-50th and 10-13rd base of read2
Nextera adaptor sequences were trimmed from 3’ of DNA libraries, Poly-dT sequences were trimmed from 3’ of RNA libraries and low-quality reads (length < 30, quality < 20) were excluded for further analysis.
Reads were first mapped to a reference genome using STAR (version: 2.6.0a) with the combined reference genome (GRCh37 for human and GRCm38 for mouse). Duplicates were removed based on the mapped position and UMI.
Genome_build: hg19/mm10
Supplementary_files_format_and_content: tab-delimited text files include cell embeddings for each cell.

organism:
Homo sapiens
Mus musculus

source_name: Cell line

growth_protocol: HEK293T (human), HepG2 (human) and NIH/3T3 (mouse) cells were cultured according to standard procedures in Dulbecco’s Modified Eagles’ Medium (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific) and 1% penicillin–streptomycin (Thermo Fisher Scientific) at 37 °C with 5% CO2.

extract_protocol:
Male C57BL/6J mice were purchased from Jackson laboratories at 8 weeks of age and maintained in the Salk animal barrier facility on 12 hr dark-light cycles with food ad libitum for four weeks before dissection. Cerebral cortex was dissected and snap-frozen in dry ice. All protocols were approved by the Salk Institute’s Institutional Animal Care and Use Committee (IACUC).
Libraries were constructed by Paired-seq workflow.

treatment_protocol: HepG2 and 3T3 cells were harvested by centrifugation, washed with PBS (Thermo Fisher Scientific) and counted using BioRad TC20 cell counter. The percentage of live cells should higher than 95%. The cells were then resuspended in cold Lysis Buffer (10 mM Tris-HCl pH 7.4 (Sigma), 10 mM NaCl (Sigma), 3 mM MgCl2 (Sigma), 0.1% IGEPAL CA-630 (Sigma)) and centrifuged for 15 min at 600 g, 4 °C. For the species mixing experiment, nuclei were then washed with PBS and resuspended, counted using BioRad TC20 cell counter. HepG2 and 3T3 nuclei were then mixed in equal proportions and applied to Paired-seq.

value: cell line


title: Control_3

value: No treatment


title: Control_1


title: LuxR_ChIP

tag: antibody


title: 12-0160 MigR1-Control NSC p9

value: MTAP deleted


title: Cell Mix DNA

tag: tissue


title: H-NS_ChIP

tag: genotype


title: U251MG Parental NSC P10


title: 13-0302 MigR1-Control NSC p11


title: Control_2


title: NHA OMRP-1 0.37EPZ015666

value: MTAP expressed (PRMT5 inhibited)


title: U251MG MTAP KO66 NSC p12


title: 7188 genomic DNA

status: Public on Oct 31 2019

city: nottingham

first: Rachel

last: Clifford

address: Biodiscovery Institute 3

institute: University of Nottingham

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Idat files were exported from the Illumina HiScan into R using the minfi package for quality control and analysis.

label: Cy3, Cy5

source_name: Airway Epithelial Cell

label_protocol: standard Illumina protocol

growth_protocol: Grown to confluence, serum starved for 24 hours and then collected

extract_protocol: Qiagen AllPrep kit

treatment_protocol: Basal

tag: disease state

value: Asthmatic

tag: status

value: Current

tag: technique

value: Pronase

value: F


title: 7279 genomic DNA

value: Healthy

value: Non

value: M


title: als09006_9_9 genomic DNA

value: Ex

value: Brush


title: azad08_1_10 genomic DNA


title: 1111_25TH genomic DNA


title: 7297 genomic DNA


title: d10_26_8 genomic DNA


title: do3 genomic DNA


title: HBEC_7219 genomic DNA


title: 1210 genomic DNA


title: 21109_25 genomic DNA


title: 7229 genomic DNA


title: c04 genomic DNA


title: do4_30_08 genomic DNA


title: 7298 genomic DNA


title: 7259 genomic DNA


title: 7293 genomic DNA


title: c06_27_9 genomic DNA


title: c11_19_8 genomic DNA


title: glioblastoma_HD_282

city: Heidelberg

first: Tobias

last: Kessler

address: Im Neuenheimer Feld 280

institute: DKFZ

hyb_protocol: bisulphite conerted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC/450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software v3.2.
Average Beta normalized with a BMIQ method.

label: Cy3 and Cy5

source_name: glioblastoma

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from FFPE tissue according with the Maxwell 16 FFPE Plus LEV DNA Kit according to standard instructions

value: glioblastoma

tag: sample preparation

value: male


title: co7_30_08 genomic DNA


title: glioblastoma_HD_285


title: 7016 genomic DNA


title: glioblastoma_HD_279


title: smac_co4 genomic DNA


title: d07_23_8 genomic DNA


title: c09_23_8 genomic DNA


title: c12 genomic DNA


title: glioblastoma_HD_277

value: female


title: glioblastoma_HD_276


title: 7294 genomic DNA


title: glioblastoma_HD_275


title: 7296 genomic DNA


title: glioblastoma_HD_274


title: glioblastoma_HD_271


title: glioblastoma_HD_273


title: glioblastoma_HD_269


title: glioblastoma_HD_270


title: glioblastoma_HD_268


title: glioblastoma_HD_264


title: glioblastoma_HD_262


title: glioblastoma_HD_265


title: glioblastoma_HD_266


title: glioblastoma_HD_261


title: glioblastoma_HD_263


title: 7220 genomic DNA


title: 7179 genomic DNA


title: glioblastoma_HD_260


title: glioblastoma_HD_267


title: glioblastoma_HD_259


title: glioblastoma_HD_256


title: glioblastoma_HD_257


title: glioblastoma_HD_258


title: 7017 genomic DNA


title: 12-0160 MigR1-MTAP NSC p7

value: Female

value: MTAP expressed


title: glioblastoma_HD_249


title: glioblastoma_HD_250


title: glioblastoma_HD_251


title: glioblastoma_HD_252


title: glioblastoma_HD_246


title: glioblastoma_HD_245


title: glioblastoma_HD_244


title: glioblastoma_HD_254


title: glioblastoma_HD_243


title: glioblastoma_HD_242


title: glioblastoma_HD_247


title: glioblastoma_HD_240


title: 7232 genomic DNA


title: glioblastoma_HD_238


title: glioblastoma_HD_237


title: glioblastoma_HD_239


title: glioblastoma_HD_235


title: glioblastoma_HD_236


title: glioblastoma_HD_241


title: glioblastoma_HD_233


title: glioblastoma_HD_232


title: glioblastoma_HD_248


title: glioblastoma_HD_231


title: glioblastoma_HD_228


title: glioblastoma_HD_230


title: glioblastoma_HD_227


title: glioblastoma_HD_234


title: glioblastoma_HD_226


title: glioblastoma_HD_229


title: 7218 genomic DNA


title: glioblastoma_HD_224


title: glioblastoma_HD_222


title: glioblastoma_HD_221


title: F1p

city: chengdu

first: qiang

middle: guo

last: zhu

state: sichuan

address: yihuanlu nanyiduan 24hao

institute: sichuan university

data_processing:
With Tophat v2.0.12 as a mapping tool, clean reads filtered out from raw reads were retained and mapped to the reference genome of Gallus gallus at ftp://ftp.ensembl.org/pub/release-72/fasta/gallus_gallus/dna.
HTSeq v0.6.1 was used to count the reads mapped to each gene. Due to the effect of sequencing depth and gene length for the reads count, FPKM was employed in present study as key parameter for the gene expression analyses.
Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed by GOSeq Release2.12 and KOBAS v2.0 respectively.
Genome_build: Ensembl release-72
Supplementary_files_format_and_content: FPKM

organism: Gallus gallus

source_name: granulosa cell

extract_protocol:
Granulose cells were removed and frozen in RNAzol. the granulosa cells were isolated from 6 mm, F5 and F1 follicles on ice and dispersed in RNAzol reagent (Molecular Research Center, Cincinnati, OH, USA). The total RNAs were extracted according to the manufacturer’s instructions and dissolved in diethylpyrocarbonate-treated H2O.
RNA quantity and quality were assessed using a Nanodrop spectrophotometer and Agilent 2100 according to the manufacturer’s instructions. Briefly, the mRNA from total RNA (at least 3 μg) were enriched by poly-A oligo attached magnetic beads with an integrity value＞8.0. Double-stranded complementary DNAs were synthesized with random hexamer primers and purified with AMPure XP beads. The inserts with expected size were concentrated and subjected for the analyses.

tag: cell type

value: natural proximal granulosa cell in F1 follicle

value: ovray


title: F1d

value: natural distal granulosa cell in F1 follicle


title: D5d

value: natural distal granulosa cell in F5 follicle


title: glioblastoma_HD_220


title: C5p

value: natural proximal granulosa cell in F5 follicle


title: glioblastoma_HD_218


title: glioblastoma_HD_217


title: glioblastoma_HD_219


title: glioblastoma_HD_215


title: glioblastoma_HD_216


title: glioblastoma_HD_214


title: glioblastoma_HD_225


title: glioblastoma_HD_213


title: glioblastoma_HD_223


title: glioblastoma_HD_210


title: glioblastoma_HD_211


title: glioblastoma_HD_209


title: glioblastoma_HD_208


title: glioblastoma_HD_207


title: glioblastoma_HD_206


title: LRRK2-GS+tunicamycin 3

city: Suwon

first: jeehoon

last: lee

state: Gyoungido

address: San5, Woncheondong

department: Pharmacology

institute: Ajou university, School of Medicine

description: Gene expression data from tunicamycin-trated LRRK2-GS astrocytes

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

source_name: LRRK2-GS astrocytes

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: Primary astrocytes were prepared by trypsinization. To deplete microglia and meningeal cells, astrocytes were incubated with serum-free DMEM for 2 days before use

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Astrocytes from LRRK2-WT and -GS mice were treated 0.2 μg/ml tunicamycin for 3 h

tag: cell

value: astrocytes


title: LRRK2-GS+tunicamycin 2


title: LRRK2-WT+tunicamycin 1

description: Gene expression data from tunicamycin-trated LRRK2-WT astrocytes

source_name: LRRK2-WT astrocytes


title: mouse Fibroblasts high TMRE content, rep4_high

first: Zhisheng

last: Jiang

state: Beijing

address: No.5 Yiheyuan Road

department: Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences

institute: Peking University

description: 2018 TMRE FIB_4_high

data_processing:
Quantification of transcript abundances from bulk RNASeq data. Software: kallisto. Version: 0.42.3
Supplementary_files_format_and_content: Processed files are h5 files with the abundance of each gene in the sample in TPM (transcripts per million) and .tsv files with est_count and tpm

source_name: Mouse Embryonic Fibroblasts

growth_protocol:
cultured for 2 days
Mouse embryonic fibroblasts (MEFs) were routinally maintained in DMEM supplemented with 10% serum (LifeTech), HEPES (ThermoFisher), Sodium Pyrivate (ThermoFisher), non-essential amminoacids (ThermoFisher), 1x penicillin-streptomycin (PanBiotech), 2-mercaptoethanol(ThermoFisher).
Mouse embryonic stem cell line (EL16.7) was routinally maintained in 2i/LIF medium contains a 1:1 mixture of  DMEM/F12 supplemented with N2 (LifeTech) and neurobasal media (LifeTech) supplemented with glutamine (LifeTech), B27 (LifeTech), insulin (Sigma), 1x penicillin-streptomycin (PanBiotech), 2-mercaptoethanol (ThermoFisher), LIF (Orfgenetics), PD0325901(Sigma)  and CHIR9021 (Deltaclon).

extract_protocol: Total RNA was extracted from each sample with the Maxwell RNA Purification Kit (Promega) according to manufacturer's instructions

treatment_protocol:
Cells were stained with 10uM CFSE for 20min at 37C and sorted after 24h
Cells were stained with 10uM CFSE for 20min at 37C. The day after they were stained with Hoechst (LifeTech) and 50nM TMRE was added to the cell culture media for 20 minutes at 37 ̊C.

value: Mouse Embryonic Fibroblasts

tag: facs bin

value: P8 low


title: mouse Fibroblasts low TMRE content, rep4_low

description: 2018 TMRE FIB_4_low

value: P10 high


title: LRRK2-GS+tunicamycin 1


title: glioblastoma_HD_205


title: LRRK2-WT+tunicamycin 2


title: mouse Fibroblasts low TMRE content, rep3_low

description: 2018 TMRE FIB_3_low


title: glioblastoma_HD_204


title: glioblastoma_HD_203


title: mouse Fibroblasts high TMRE content, rep3_high

description: 2018 TMRE FIB_3_high


title: glioblastoma_HD_202


title: glioblastoma_HD_212


title: mouse Fibroblasts low TMRE content, rep2_low

description: 2018 TMRE FIB_2_low


title: glioblastoma_HD_201


title: mouse Fibroblasts high TMRE content, rep1_high

description: 2018 TMRE FIB_1_high


title: glioblastoma_HD_199


title: glioblastoma_HD_278


title: glioblastoma_HD_198


title: mouse ESCs high TMRE content, rep4_high

description: 2018 TMRE ES_4_high

source_name: Mouse Embryonic Stem Cells

growth_protocol:
cultured for 2 days in the presence of LIF
Mouse embryonic fibroblasts (MEFs) were routinally maintained in DMEM supplemented with 10% serum (LifeTech), HEPES (ThermoFisher), Sodium Pyrivate (ThermoFisher), non-essential amminoacids (ThermoFisher), 1x penicillin-streptomycin (PanBiotech), 2-mercaptoethanol(ThermoFisher).
Mouse embryonic stem cell line (EL16.7) was routinally maintained in 2i/LIF medium contains a 1:1 mixture of  DMEM/F12 supplemented with N2 (LifeTech) and neurobasal media (LifeTech) supplemented with glutamine (LifeTech), B27 (LifeTech), insulin (Sigma), 1x penicillin-streptomycin (PanBiotech), 2-mercaptoethanol (ThermoFisher), LIF (Orfgenetics), PD0325901(Sigma)  and CHIR9021 (Deltaclon).

value: Mouse Embryonic Stem Cells


title: mouse ESCs low TMRE content, rep3_low

description: 2018 TMRE ES_3_low


title: mouse ESCs low TMRE content, rep4_low

description: 2018 TMRE ES_4_low


title: mouse ESCs high TMRE content, rep3_high

description: 2018 TMRE ES_3_high


title: mouse Fibroblasts low TMRE content, rep1_low

description: 2018 TMRE FIB_1_low


title: glioblastoma_HD_195


title: glioblastoma_HD_200


title: glioblastoma_HD_194


title: mouse Fibroblasts medium-fast proliferating, fast

description: 2018 CFSE FIB_ML fast

growth_protocol:
cultured for 5 days
Mouse embryonic fibroblasts (MEFs) were routinally maintained in DMEM supplemented with 10% serum (LifeTech), HEPES (ThermoFisher), Sodium Pyrivate (ThermoFisher), non-essential amminoacids (ThermoFisher), 1x penicillin-streptomycin (PanBiotech), 2-mercaptoethanol(ThermoFisher).
Mouse embryonic stem cell line (EL16.7) was routinally maintained in 2i/LIF medium contains a 1:1 mixture of  DMEM/F12 supplemented with N2 (LifeTech) and neurobasal media (LifeTech) supplemented with glutamine (LifeTech), B27 (LifeTech), insulin (Sigma), 1x penicillin-streptomycin (PanBiotech), 2-mercaptoethanol (ThermoFisher), LIF (Orfgenetics), PD0325901(Sigma)  and CHIR9021 (Deltaclon).

value: P4 high


title: mouse Fibroblasts medium-slow proliferating, slow

description: 2018 CFSE FIB_MH slow

value: P4 slow


title: mouse ESCs high TMRE content, rep2_high

description: 2018 TMRE ES_2_high


title: mouse ESCs low TMRE content, rep1_low

description: 2018 TMRE ES_1_low


title: glioblastoma_HD_193

value: glioblastoma


title: mouse ESCs high TMRE content, rep1_high

description: 2018 TMRE ES_1_high


title: glioblastoma_HD_191

value: male


title: glioblastoma_HD_189

value: female


title: glioblastoma_HD_190


title: glioblastoma_HD_192


title: glioblastoma_HD_196


title: mouse ESCs low TMRE content, rep2_low

description: 2018 TMRE ES_2_low


title: glioblastoma_HD_272


title: glioblastoma_HD_188


title: mouse ESCs medium-fast proliferating, fast

description: 2018 CFSE ES_ML fast

growth_protocol:
cultured for 3 days in the presence of LIF
Mouse embryonic fibroblasts (MEFs) were routinally maintained in DMEM supplemented with 10% serum (LifeTech), HEPES (ThermoFisher), Sodium Pyrivate (ThermoFisher), non-essential amminoacids (ThermoFisher), 1x penicillin-streptomycin (PanBiotech), 2-mercaptoethanol(ThermoFisher).
Mouse embryonic stem cell line (EL16.7) was routinally maintained in 2i/LIF medium contains a 1:1 mixture of  DMEM/F12 supplemented with N2 (LifeTech) and neurobasal media (LifeTech) supplemented with glutamine (LifeTech), B27 (LifeTech), insulin (Sigma), 1x penicillin-streptomycin (PanBiotech), 2-mercaptoethanol (ThermoFisher), LIF (Orfgenetics), PD0325901(Sigma)  and CHIR9021 (Deltaclon).


title: mouse Fibroblasts slow-slow proliferating, slow

description: 2018 CFSE FIB_HH slow

value: P5 slow


title: mouse Fibroblasts slow-fast proliferating, fast

description: 2018 CFSE FIB_HL fast

value: P5 fast


title: glioblastoma_HD_187


title: glioblastoma_HD_186


title: mouse ESCs medium-slow proliferating, slow

description: 2018 CFSE ES_MH slow


title: mouse ESCs slow-fast proliferating, fast

description: 2018 CFSE ES_HL fast


title: glioblastoma_HD_185


title: glioblastoma_HD_255


title: glioblastoma_HD_183


title: glioblastoma_HD_184


title: glioblastoma_HD_182


title: mouse ESCs slow-slow proliferating, slow

description: 2018 CFSE ES_HH slow


title: mouse Fibroblasts medium proliferating, rep2 medium

description: 2016 FIB_5 rep2 medium

value: P8 med


title: glioblastoma_HD_178


title: mouse Fibroblasts medium proliferating, rep1 medium

description: 2016 FIB_2 rep1 medium


title: glioblastoma_HD_179


title: mouse Fibroblasts fast proliferating, rep2 fast

description: 2016 FIB_6 rep2 fast

value: P9 fast


title: mouse ESCs fast proliferating, rep2 fast

description: 2016 ES_6 rep2 fast


title: mouse Fibroblasts fast proliferating, rep1 fast

description: 2016 FIB_3 rep1 fast


title: mouse Fibroblasts slow proliferating, rep2 slow

description: 2016 FIB_4 rep2 slow


title: glioblastoma_HD_177


title: glioblastoma_HD_181


title: mouse Fibroblasts slow proliferating, rep1 slow

description: 2016 FIB_1 rep1 slow


title: glioblastoma_HD_176


title: mouse ESCs medium proliferating, rep2 medium

description: 2016 ES_5 rep2 medium


title: glioblastoma_HD_174


title: glioblastoma_HD_175


title: mouse ESCs slow proliferating, rep2 slow

description: 2016 ES_4 rep2 slow


title: glioblastoma_HD_180


title: glioblastoma_HD_173


title: mouse ESCs medium proliferating, rep1 medium

description: 2016 ES_2 rep1 medium


title: glioblastoma_HD_172


title: mouse ESCs slow proliferating, rep1 slow

description: 2016 ES_1 rep1 slow


title: glioblastoma_HD_197


title: glioblastoma_HD_168


title: glioblastoma_HD_167


title: glioblastoma_HD_170


title: glioblastoma_HD_169


title: glioblastoma_HD_171


title: glioblastoma_HD_164


title: glioblastoma_HD_163


title: glioblastoma_HD_165


title: glioblastoma_HD_166


title: mouse ESCs fast proliferating, rep1 fast

description: 2016 ES_3 rep1 fast


title: glioblastoma_HD_152


title: glioblastoma_HD_154


title: glioblastoma_HD_149


title: glioblastoma_HD_153


title: glioblastoma_HD_162


title: glioblastoma_HD_158


title: glioblastoma_HD_155


title: glioblastoma_HD_156


title: glioblastoma_HD_159


title: glioblastoma_HD_148


title: glioblastoma_HD_157


title: glioblastoma_HD_147


title: glioblastoma_HD_146


title: glioblastoma_HD_145


title: glioblastoma_HD_144


title: glioblastoma_HD_142


title: glioblastoma_HD_150


title: glioblastoma_HD_141


title: 7185 genomic DNA

value: Healthy

value: Non

value: Pronase

value: M

tag: age


title: glioblastoma_HD_160

tag: gender


title: glioblastoma_HD_143


title: glioblastoma_HD_161


title: glioblastoma_HD_139


title: glioblastoma_HD_138


title: glioblastoma_HD_136


title: glioblastoma_HD_151


title: glioblastoma_HD_137


title: glioblastoma_HD_134


title: glioblastoma_HD_135


title: glioblastoma_HD_140


title: glioblastoma_HD_132


title: glioblastoma_HD_133


title: glioblastoma_HD_130


title: glioblastoma_HD_131


title: glioblastoma_HD_129


title: glioblastoma_HD_123


title: glioblastoma_HD_126


title: glioblastoma_HD_125


title: glioblastoma_HD_127


title: glioblastoma_HD_122


title: glioblastoma_HD_120


title: glioblastoma_HD_119


title: glioblastoma_HD_117


title: glioblastoma_HD_115


title: glioblastoma_HD_116


title: glioblastoma_HD_114


title: glioblastoma_HD_113


title: glioblastoma_HD_111


title: glioblastoma_HD_112


title: glioblastoma_HD_128


title: glioblastoma_HD_106


title: glioblastoma_HD_107


title: glioblastoma_HD_108


title: glioblastoma_HD_124


title: glioblastoma_HD_102


title: glioblastoma_HD_121


title: glioblastoma_HD_110


title: glioblastoma_HD_109


title: glioblastoma_HD_101


title: glioblastoma_HD_097


title: glioblastoma_HD_099


title: glioblastoma_HD_104


title: glioblastoma_HD_100


title: glioblastoma_HD_105


title: glioblastoma_HD_095


title: glioblastoma_HD_096


title: glioblastoma_HD_094


title: glioblastoma_HD_093


title: glioblastoma_HD_118


title: glioblastoma_HD_092


title: glioblastoma_HD_091


title: glioblastoma_HD_087


title: glioblastoma_HD_089


title: glioblastoma_HD_088


title: glioblastoma_HD_090


title: glioblastoma_HD_086


title: glioblastoma_HD_103


title: glioblastoma_HD_085


title: glioblastoma_HD_080


title: glioblastoma_HD_079


title: glioblastoma_HD_081


title: glioblastoma_HD_074


title: glioblastoma_HD_084


title: glioblastoma_HD_075


title: glioblastoma_HD_069


title: glioblastoma_HD_072


title: glioblastoma_HD_098


title: glioblastoma_HD_071


title: glioblastoma_HD_083


title: glioblastoma_HD_073


title: glioblastoma_HD_066


title: glioblastoma_HD_078


title: glioblastoma_HD_065


title: glioblastoma_HD_064


title: glioblastoma_HD_082


title: glioblastoma_HD_063


title: glioblastoma_HD_059


title: glioblastoma_HD_060


title: glioblastoma_HD_077


title: glioblastoma_HD_057


title: glioblastoma_HD_062


title: glioblastoma_HD_056


title: glioblastoma_HD_076


title: glioblastoma_HD_070


title: glioblastoma_HD_058


title: glioblastoma_HD_055


title: glioblastoma_HD_052


title: glioblastoma_HD_054


title: glioblastoma_HD_053


title: glioblastoma_HD_068


title: glioblastoma_HD_067


title: glioblastoma_HD_045


title: glioblastoma_HD_043


title: glioblastoma_HD_051


title: glioblastoma_HD_048


title: glioblastoma_HD_050


title: glioblastoma_HD_042


title: glioblastoma_HD_047


title: glioblastoma_HD_041


title: glioblastoma_HD_040


title: glioblastoma_HD_061


title: glioblastoma_HD_039


title: glioblastoma_HD_038


title: glioblastoma_HD_037


title: glioblastoma_HD_035


title: glioblastoma_HD_034


title: glioblastoma_HD_032


title: glioblastoma_HD_049


title: glioblastoma_HD_036


title: glioblastoma_HD_024


title: glioblastoma_HD_028


title: glioblastoma_HD_027


title: glioblastoma_HD_029


title: glioblastoma_HD_046


title: glioblastoma_HD_026


title: glioblastoma_HD_030


title: glioblastoma_HD_033


title: glioblastoma_HD_025


title: glioblastoma_HD_031


title: glioblastoma_HD_018


title: glioblastoma_HD_044


title: glioblastoma_HD_022


title: glioblastoma_HD_020


title: glioblastoma_HD_019


title: glioblastoma_HD_023


title: NELF-E WT Rep1

city: Newark

first: Jean-Pierre

last: Etchegaray

state: NJ

address: 225 University Ave

department: Biological Sciences

institute: Rutgers University

description: CUT&RUN assay

data_processing:
Reads were aligned to mm9 using BWA 0.7.4, and PCR duplicates were removed by samtools.
bigWig files were generated by bamCoverage in Deeptools.
Genome_build: mm9

source_name: mouse embryonic stem cells

growth_protocol: ESCs were grown under standard conditions in DMEM supplemented with 10% fetal bovine serum, LIF, glutamine, pen-strep, and beta-mercaptoethanol.

extract_protocol:
For H3K36me3, H3K79me2 and Pol II ChIP-seq experiments: approximately 5x10^7 formaldehyde-crosslinked ESCs were lysed with IP-Star (Diagenode) buffer. Chromatin was sonicated on the Bioruptor (Diagenode) to an average size of 0.2-1 kb. ChIP was performed on chromatin from approximately 5 million cells with 3 μg of antibody (above) using the IP-Star Automated System (Diagenode), and 2.5% of chromatin was used for each whole cell extract (WCE). Following reversal of crosslinks, sample and WCE DNA was purified. ChIP DNA was dissolved in water and placed on the SPRI-TE (Beckman Coulter) for Illumina sample preparation. For H3K9ac, H3K56ac and LEO1 ChIP-seq experiements: approximately 5x10^7 formaldehyde-crosslinked ESCs were lysed and prepared for ChIP-seq according to the protocol described by Black et al., (2013) (PMID: 23871696).
For H3K9ac, H3K56ac and LEO1 ChIP-seq experiments: libraries were constructued according to the protocol described by TruSeq ChIP Sample ptreparation from Illumina Part# 15023092 Rev.B, Cat# IP-202-9001DOC.

value: Embryonic stem cells

value: Wild-type

tag: passages

value: Passage 21

value: Mouse strain:129 SvJae F1

tag: chip antibody

value: NELF-E (Abcam, cat# ab28038)


title: LEO1 Sirt6-KO Rep2

tag: treatment

value: SIRT6-Knock Out

tag: strain

value: LEO1 (Bethyl Laboratories. Inc, cat# A300-175A)


title: LEO1 Sirt6-KO Rep1


title: glioblastoma_HD_017

value: glioblastoma

value: male


title: NELF-E Sirt6-KO Rep1

description: CUT&RUN assay


title: LEO1 WT Rep2


title: glioblastoma_HD_016


title: LEO1 WT Rep1


title: glioblastoma_HD_021

value: female


title: glioblastoma_HD_013


title: H3K56ac Sirt6-KO Rep1

value: H3K56ac (Abcam, cat# ab76307)


title: glioblastoma_HD_011


title: H3K56ac Sirt6-KO Rep2


title: glioblastoma_HD_012


title: H3K56ac WT Rep2


title: glioblastoma_HD_014


title: H3K9ac Sirt6-KO Rep1

value: H3K9ac (Millipore, cat# 07-352)


title: H3K9ac Sirt6-KO Rep2


title: glioblastoma_HD_015


title: glioblastoma_HD_006


title: glioblastoma_HD_005


title: glioblastoma_HD_007


title: H3K9ac WT Rep2


title: glioblastoma_HD_009


title: H3K79me2 Sirt6-KO Rep2

value: H3K79me2 (Cell Signaling Technologies, cat# 5427)


title: H3K9ac WT Rep1


title: glioblastoma_HD_008


title: glioblastoma_HD_004


title: glioblastoma_HD_010


title: H3K79me2 WT Rep1


title: glioblastoma_HD_002


title: H3K36me3 Sirt6-KO Rep2

value: H3K36me3 (Cell Signaling Technologies, cat# 4909)


title: H3K79me2 Sirt6-KO Rep1


title: H3K36me3 Sirt6-KO Rep1


title: H3K56ac WT Rep1


title: glioblastoma_HD_003


title: H3K36me3 WT Rep2


title: glioblastoma_HD_001


title: H3K36me3 WT Rep1


title: Pol II Sirt6-KO Rep2

value: Pol II (Cell Signaling Technologies, cat# 2629)


title: H3K79me2 WT Rep2


title: Pol II Sirt6-KO Rep1


title: Pol II WT Rep3


title: Pol II WT Rep1


title: Pol II WT Rep2


title: glioblastoma_HD_379


title: glioblastoma_HD_378


title: glioblastoma_HD_377


title: glioblastoma_HD_375


title: glioblastoma_HD_374


title: glioblastoma_HD_372


title: glioblastoma_HD_373


title: glioblastoma_HD_371


title: glioblastoma_HD_380


title: glioblastoma_HD_369


title: glioblastoma_HD_368


title: glioblastoma_HD_367


title: glioblastoma_HD_370


title: glioblastoma_HD_376


title: glioblastoma_HD_366


title: A549-sh_CNOT2

city: Seoul

first: Miyong

last: Yun

address: 209, Neungdong-ro, Gwangjin-gu

department: Bioindustry and bioresource engineering

institute: Sejong University

description: Gene expression after establisement of cell lines stably expressing CNOT2 gene in shRNA plasmid

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Human Oligo Microarray (60K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

source_name: A549-CNOT2 K/D

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: A549 cells were cultured in RPMI-1640 (Corning, Manassas, VA, USA), supplemented with 10% Fetal Bovine Serum (FBS; Corning, Manassas, VA, USA) and 1% penicillin-streptomycin (Corning, Manassas, VA, USA).  All cells were cultured in a 37℃ humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: After transfection of pRS vector containing CNOT2 shRNA or control shRNA, A549 cells were selected with 1.5 ug/ml puromycin for 3 days. And then cells were cultured with normal media

tag: cell line

tag: genotype/variation

value: CNOT2 knockdown

value: Non-small cell lung cancer cell line


title: glioblastoma_HD_365

tag: tissue


title: A549-sh_con

description: Gene expression after establisement of cell lines stably expressing control gene (empty vector) in shRNA plasmid

value: control


title: glioblastoma_HD_364


title: glioblastoma_HD_357


title: glioblastoma_HD_358


title: glioblastoma_HD_361


title: glioblastoma_HD_363


title: glioblastoma_HD_360


title: glioblastoma_HD_359


title: brain_malignantglioma_NOA-08_095

description: tumor

data_processing: BeadStudio software v3.2. Average Beta values normalized with a BMIQ method.

source_name: malignant glioma

extract_protocol: Genomic DNA was extracted and pruified from FFPE tissue according with the Maxwell 16 FFPE Plus LEV DNA Kit according to standard instructions

tag: who grade


title: glioblastoma_HD_353


title: glioblastoma_HD_356


title: brain_malignantglioma_NOA-08_091

description: tumor


title: glioblastoma_HD_351


title: glioblastoma_HD_355


title: brain_malignantglioma_NOA-08_039

description: tumor


title: brain_malignantglioma_NOA-08_098

description: tumor


title: brain_malignantglioma_NOA-08_063

description: tumor


title: brain_malignantglioma_NOA-08_092

description: tumor


title: glioblastoma_HD_350


title: brain_malignantglioma_NOA-08_021

description: tumor


title: glioblastoma_HD_352


title: brain_malignantglioma_NOA-08_061

description: tumor


title: brain_malignantglioma_NOA-08_040

description: tumor


title: brain_malignantglioma_NOA-08_036

description: tumor


title: brain_malignantglioma_NOA-08_022

description: tumor


title: brain_malignantglioma_NOA-08_057

description: tumor


title: brain_malignantglioma_NOA-08_053

description: tumor


title: glioblastoma_HD_341


title: M2 RNA-seq 1

first: Xu

last: Wang

address: No. 12 Zhongguancun south road

institute: Institute of crop sciences, CAAS

description: transcriptome profiling of M2

data_processing:
The paired end reads were aligned to genome sequences using TopHat (Trapnell et al., 2009) allowing up to two mismatches. Splice junction sequences required at least four bases on each side of the junction. Reads mapped to multiple locations as well as only uniquely mapped reads were used and compared with each other to avoid the improper deletion of reads for subsequent analysis.
Genome_build: Arabidopisis
Supplementary_files_format_and_content: wig files were generated using MACS program

source_name: 12-day-old hos1-3 seedlings grown in long days

growth_protocol: In the method of plant cell paper

extract_protocol:
Total RNAs were extracted from 12-day-old seedlings of wild type (WT), M1 (nup96-1) and M2 (hos1-3)
RNA-seq dUTP protocal

treatment_protocol: No treatment

value: seedlings


title: glioblastoma_HD_340


title: M2 RNA-seq 2

description: transcriptome profiling of M2


title: brain_malignantglioma_NOA-08_059

description: tumor


title: M2 RNA-seq 3

description: transcriptome profiling of M2


title: brain_malignantglioma_NOA-08_019

description: tumor


title: glioblastoma_HD_362


title: glioblastoma_HD_345


title: brain_malignantglioma_NOA-08_035

description: tumor


title: glioblastoma_HD_346


title: glioblastoma_HD_343


title: glioblastoma_HD_344


title: glioblastoma_HD_342


title: glioblastoma_HD_338


title: glioblastoma_HD_339


title: M1 RNA-seq 1

description: transcriptome profiling of M1

source_name: 12-day-old nup96-1 seedlings grown in long days


title: M1 RNA-seq 2

description: transcriptome profiling of M1


title: WT RNA-seq 3

description: transcriptome profiling of WT (wild type)

source_name: 12-day-old Col-0 seedlings grown in long days

value: wild type